{
  "abstract": "Ribo-seq has provided compelling evidence that there are many translated but unannotated ORFs. Despite a growing body of peptidomic support for cryptic ORFs, the computational discovery of weakly translated, short and mutually overlapping ORFs has remained a major bottleneck. Here we introduce PRICE 2, a method designed to resolve these challenging translation events by adapting concepts from isoform deconvolution. PRICE 2 employs a generative model combined with group LASSO regularized regression to jointly infer active ORFs across multiple sequencing runs. In a comprehensive benchmark, PRICE 2 outperformed thirteen state-of-the-art tools in detecting short and overlapping ORFs. Orthogonal validation via immunopeptidomics demonstrated that ORFs identified by PRICE 2 enable the discovery of [~]40% more cryptic MHC-I peptides than the best-performing competing tool at a fixed false discovery rate. By analyzing public ribo-seq data across 45 distinct cell and tissue types, we constructed ORF-stock, a comprehensive database of non-canonical ORFs for immunopeptidomic studies.",
  "abstract_shown": true,
  "affiliations": [
    "University of Regensburg"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 3,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "K. Maidhof"
    },
    {
      "name": "A. Schlosser"
    },
    {
      "name": "F. Erhard"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/b74trpq128tsv.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.10.01.755973",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.10.01.755973v1.full",
  "id": "b74trpq128tsv",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.10.01.755973v1",
  "language": null,
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "bioinformatics"
    ],
    [
      "openalex",
      "1312|RNA and protein synthesis mechanisms"
    ]
  ],
  "openalex": "W7221028339",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.10.01.755973v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-01",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/b74trpq128tsv.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:26:38Z",
      "native_id": "10.64898/2026.10.01.755973",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.10.01.755973v2"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:bioinformatics",
      "subfield": "bioinformatics"
    }
  ],
  "title": "Robust ORF Deconvolution from Multiple Ribo-seq Datasets with Group LASSO Penalty",
  "title_text": "Robust ORF Deconvolution from Multiple Ribo-seq Datasets with Group LASSO Penalty",
  "type": "preprint",
  "updated_at": "2026-10-30T12:27:39Z",
  "url": "https://research.draconitic.com/paper/b74trpq128tsv",
  "venue": "bioRxiv",
  "versions": []
}